In the phylum Basidiomycota, a wide variety of lifestyles are represented. These range from well-known and conspicuous wood-decaying mushrooms, plant growth-promoting and mutualistic mycorrhizae, and crop-destroying smut and rust fungi, to yeast-like human pathogens. Lifestyle differences have consequences for the mating and breeding systems of these fungi (see “Glossary,” below, for definitions of specialist terms used in this article), which are reflected in the genetic evolution of mating-type determination. For over a century fungi have been recognized as having diverse breeding systems, from homothallism (i.e., universal compatibility among gametes, including among clonemates) to heterothallism (i.e., mating among haploid gametes carrying different mating-type alleles). The study of breeding systems, for example, led to the discovery of the astounding variability in mating-type alleles among mushrooms, with thousands of different mating types in some species (1), and to the realization that in many fungal pathogens the process of sexual reproduction is closely linked to infection and pathogenicity (2) (Fig. 1). The importance of basidiomycete fungi and their great research tractability, from ecology to genomics, have brought major insights into the diversification of genetic mechanisms used to achieve sexual reproduction.

General life cycles of dimorphic and mushroom-forming basidiomycetes. Three basidiomycetes are pictured where sexual reproduction and a dimorphic switch between a yeast cell and a hyphal form are crucial to infection of plant (A, B) or animal (C) hosts. The haploid yeast forms of the maize smut Ustilago maydis (A) and the anther smut Microbotryum spp. (B) are nonpathogenic and can undergo asexual mitotic vegetative growth. In Microbotryum, the yeast stage is, however, short-lived because mating occurs mostly between cells within the same tetrad. Upon mating with a compatible partner, both fungi switch to an enduring infection hyphal form (dikaryon; n + n) that can invade the host plant. Proliferation and differentiation of U. maydis(A) in the plant culminates with the production of masses of wind-dispersing diploid spores (teliospores; 2n) in large tumor-like tissues, whereas in Microbotryum(B), teliospores are formed in the anthers of infected flowers and transmitted by pollinators onto healthy plants. In the case of Cryptococcus neoformans(C), the single-celled yeast form may be free-living or mycoparasitic. A similar dimorphic switch occurs upon mating of yeast cells of opposite mating type (α or α), ultimately resulting in the infectious propagules (basidiospores) that potentially infect an animal host after dispersal. These infectious structures may also be generated by haploid selfing (depicted with gray background), where fusion occurs between homothallic cells carrying identical MAT alleles (α/α diploid is depicted) and form monokaryotic hyphae with unfused clamp connections (see text for details). In mushroom-forming fungi such as Schizophyllum commune(D), germination of haploid spores yields haploid monokaryons capable of independent growth. When two compatible monokaryons meet, a fertile clamped dikaryon is formed which develops into fruiting bodies (mushrooms) triggered upon suitable environmental cues, where basidia arise. In all these and other basidiomycetes, nuclear fusion (karyogamy) is usually delayed until the formation of basidia (or teliospores). Meiosis ensues, generating four haploid nuclei, which give rise to basidiospores to complete the cycle. Adapted from Morrow and Fraser (2) and Nieuwenhuis et al. (17) with permission of the publishers.

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Figure 1

General life cycles of dimorphic and mushroom-forming basidiomycetes. Three basidiomycetes are pictured where sexual reproduction and a dimorphic switch between a yeast cell and a hyphal form are crucial to infection of plant (A, B) or animal (C) hosts. The haploid yeast forms of the maize smut Ustilago maydis (A) and the anther smut Microbotryum spp. (B) are nonpathogenic and can undergo asexual mitotic vegetative growth. In Microbotryum, the yeast stage is, however, short-lived because mating occurs mostly between cells within the same tetrad. Upon mating with a compatible partner, both fungi switch to an enduring infection hyphal form (dikaryon; n + n) that can invade the host plant. Proliferation and differentiation of U. maydis(A) in the plant culminates with the production of masses of wind-dispersing diploid spores (teliospores; 2n) in large tumor-like tissues, whereas in Microbotryum(B), teliospores are formed in the anthers of infected flowers and transmitted by pollinators onto healthy plants. In the case of Cryptococcus neoformans(C), the single-celled yeast form may be free-living or mycoparasitic. A similar dimorphic switch occurs upon mating of yeast cells of opposite mating type (α or α), ultimately resulting in the infectious propagules (basidiospores) that potentially infect an animal host after dispersal. These infectious structures may also be generated by haploid selfing (depicted with gray background), where fusion occurs between homothallic cells carrying identical MAT alleles (α/α diploid is depicted) and form monokaryotic hyphae with unfused clamp connections (see text for details). In mushroom-forming fungi such as Schizophyllum commune(D), germination of haploid spores yields haploid monokaryons capable of independent growth. When two compatible monokaryons meet, a fertile clamped dikaryon is formed which develops into fruiting bodies (mushrooms) triggered upon suitable environmental cues, where basidia arise. In all these and other basidiomycetes, nuclear fusion (karyogamy) is usually delayed until the formation of basidia (or teliospores). Meiosis ensues, generating four haploid nuclei, which give rise to basidiospores to complete the cycle. Adapted from Morrow and Fraser (2) and Nieuwenhuis et al. (17) with permission of the publishers.

Phylogeny of the Basidiomycota indicating the breeding system and the number of MAT genes across representative species of the three subphyla. The breeding system and the different taxonomic lineages are color-coded as given in the key and are kept consistent in all figures. Gene numbers shown for each species were obtained either from previous reports (20, 41, 100) or from newly surveyed genome data (marked with a hash sign after the species name). In the Agaricomycetes, values shown in parentheses are putative non-mating-type pheromone receptors. A question mark indicates cases where information on the breeding system is not available or is uncertain (e.g., because the sexual stage of a species is unknown). A schematic representation of the P/R and HD loci is given in Fig. 3 for representative species of each lineage marked with numbers enclosed in white circles. Letters in superscript next to the number of pheromone precursor genes indicate that (a) all genes encode the same mature pheromone peptide or that (b) no CAAX motif was detected in one of the putative pheromone precursors. The species phylogenetic tree was constructed in IQ-TREE (193) using a previously described approach (194). Branch support values are shown in the tree nodes as given in the key and were assessed with the ultrafast bootstrap approximation (UFBoot) and the approximate likelihood ratio test (SH-aLRT), each with 1,000 replicates. The basidiomycete clade is rooted with sequences from Ascomycete fungi.

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Figure 2

Phylogeny of the Basidiomycota indicating the breeding system and the number of MAT genes across representative species of the three subphyla. The breeding system and the different taxonomic lineages are color-coded as given in the key and are kept consistent in all figures. Gene numbers shown for each species were obtained either from previous reports (20, 41, 100) or from newly surveyed genome data (marked with a hash sign after the species name). In the Agaricomycetes, values shown in parentheses are putative non-mating-type pheromone receptors. A question mark indicates cases where information on the breeding system is not available or is uncertain (e.g., because the sexual stage of a species is unknown). A schematic representation of the P/R and HD loci is given in Fig. 3 for representative species of each lineage marked with numbers enclosed in white circles. Letters in superscript next to the number of pheromone precursor genes indicate that (a) all genes encode the same mature pheromone peptide or that (b) no CAAX motif was detected in one of the putative pheromone precursors. The species phylogenetic tree was constructed in IQ-TREE (193) using a previously described approach (194). Branch support values are shown in the tree nodes as given in the key and were assessed with the ultrafast bootstrap approximation (UFBoot) and the approximate likelihood ratio test (SH-aLRT), each with 1,000 replicates. The basidiomycete clade is rooted with sequences from Ascomycete fungi.

Schematic showing the genomic structure and diversity of MAT loci in representative basidiomycete lineages. The genomic organization of the homeodomain (HD) and pheromone/receptor (P/R) MAT loci is shown for selected species of (A) the Agaricomycotina and (B) the Ustilaginomycotina and Pucciniomycotina. Arrows indicate genes and their direction of transcription. Putative MAT loci are shaded in light brown, and MAT genes are colored as indicated in the key with different color grades representing different alleles (or paralogs). When known, conserved genes flanking MAT loci (colored light yellow or light blue) are shown within each lineage. Genes that encode components of the pheromone response pathway are shown in pink and are in many cases within the MAT locus. Putative homologs of a protein required for posttranslational modification of pheromone precursors (isoprenyl cysteine methyltransferase [ICMT]) are colored purple and appear near the P/R locus in some species. P/R loci no longer determining mating-type specificity in bipolar Agaricomycetes are depicted with a gray background. In M. lychnidis-dioicae, the two mating-type chromosomes are highly rearranged and enriched in transposable elements, so that only a small number of genes is depicted. Of note, whereas in M. nashicola P/R and HD genes are far apart on the same chromosome, in E. vaccinii and M. endogenum the two sets of genes are closer together. Other genes or genomic features are colored or represented as given in the key. For citations and additional details, see text. Gene names or their associated protein accession numbers are shown as they appear in their respective genome databases, except in species of Ustilaginomycotina and Tremellomycetes, where names were given based on sequence identity to the closest homolog in U. maydis and C. neoformans, respectively.

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Figure 3

Schematic showing the genomic structure and diversity of MAT loci in representative basidiomycete lineages. The genomic organization of the homeodomain (HD) and pheromone/receptor (P/R) MAT loci is shown for selected species of (A) the Agaricomycotina and (B) the Ustilaginomycotina and Pucciniomycotina. Arrows indicate genes and their direction of transcription. Putative MAT loci are shaded in light brown, and MAT genes are colored as indicated in the key with different color grades representing different alleles (or paralogs). When known, conserved genes flanking MAT loci (colored light yellow or light blue) are shown within each lineage. Genes that encode components of the pheromone response pathway are shown in pink and are in many cases within the MAT locus. Putative homologs of a protein required for posttranslational modification of pheromone precursors (isoprenyl cysteine methyltransferase [ICMT]) are colored purple and appear near the P/R locus in some species. P/R loci no longer determining mating-type specificity in bipolar Agaricomycetes are depicted with a gray background. In M. lychnidis-dioicae, the two mating-type chromosomes are highly rearranged and enriched in transposable elements, so that only a small number of genes is depicted. Of note, whereas in M. nashicola P/R and HD genes are far apart on the same chromosome, in E. vaccinii and M. endogenum the two sets of genes are closer together. Other genes or genomic features are colored or represented as given in the key. For citations and additional details, see text. Gene names or their associated protein accession numbers are shown as they appear in their respective genome databases, except in species of Ustilaginomycotina and Tremellomycetes, where names were given based on sequence identity to the closest homolog in U. maydis and C. neoformans, respectively.

Phylogeny of Basidiomycota pheromone receptor proteins. Amino acid sequences identified by BLAST from publicly available databases or from genome projects were retrieved for representative species of the tree subphyla of the Basidiomycota. A total of 106 sequences were manually inspected, amended where necessary, and aligned with MAFFT (195), and poorly aligned regions were trimmed with trimAl (196). The phylogenetic tree and branch support were obtained as in Fig. 2, and the tree was rooted with S. cerevisiae Ste3p. GenBank accession numbers (*), Joint Genome Institute protein identifiers (**), and RIKEN/NBRP identifiers (***) are given after the strain name, with letters in superscript indicating (a) genomes assembled from available raw sequencing data and inspected locally, (b) genomic contigs/scaffolds lacking gene annotation, and (c) genes whose annotation was corrected. Species highlighted in boldface are shown in Fig. 3, with arrows before their names indicating the allelic version (or paralog) of the pheromone receptor as colored in Fig. 3. Of note, the STE3.1 and STE3.2 alleles in the Microbotryomycetes (Pucciniomycotina) displayed the deepest allelic divergence and trans-specific polymorphism, with the STE3.1 alleles of the different species branching together rather than each of these alleles clustering with the STE3.2 allele from the same species (42, 45, 137).

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Figure 4

Phylogeny of Basidiomycota pheromone receptor proteins. Amino acid sequences identified by BLAST from publicly available databases or from genome projects were retrieved for representative species of the tree subphyla of the Basidiomycota. A total of 106 sequences were manually inspected, amended where necessary, and aligned with MAFFT (195), and poorly aligned regions were trimmed with trimAl (196). The phylogenetic tree and branch support were obtained as in Fig. 2, and the tree was rooted with S. cerevisiae Ste3p. GenBank accession numbers (*), Joint Genome Institute protein identifiers (**), and RIKEN/NBRP identifiers (***) are given after the strain name, with letters in superscript indicating (a) genomes assembled from available raw sequencing data and inspected locally, (b) genomic contigs/scaffolds lacking gene annotation, and (c) genes whose annotation was corrected. Species highlighted in boldface are shown in Fig. 3, with arrows before their names indicating the allelic version (or paralog) of the pheromone receptor as colored in Fig. 3. Of note, the STE3.1 and STE3.2 alleles in the Microbotryomycetes (Pucciniomycotina) displayed the deepest allelic divergence and trans-specific polymorphism, with the STE3.1 alleles of the different species branching together rather than each of these alleles clustering with the STE3.2 allele from the same species (42, 45, 137).

Roles of P/R and HD genes on the formation and maintenance of the dikaryon in C. cinerea. Pheromone signaling is not required to attract mates, and hyphal fusion is mating-type independent (diagram 1). Upon fusion, nuclei enter the mycelium of the other mate and migrate until they reach a hyphal tip cell (diagram 2). During hyphal tip elongation, the two types of haploid nuclei (depicted in white and black, representing different MAT genotypes) pair at the tip cell (diagram 3), and at the place where mitosis will take place, a hook-like structure (called a clamp connection) is formed (diagram 4). The two nuclei divide synchronously: one of the nuclei divides in the direction of the clamp cell that is growing backward toward the main hyphae, while the other divides along the main hyphal axis (diagram 5). Septa are generated between the dividing nuclei. This way one nucleus stays temporarily entrapped in the clamp cell, one nucleus of the other type is enclosed in the newly formed subapical cell, and a nucleus of each type is maintained in the emerging hyphal tip cell (diagram 6). The clamp cell fuses with the subapical cell and releases the entrapped nucleus from the clamp cell, restoring the dikaryotic state of the subapical cell (diagram 7). In C. cinerea, steps controlled by P/R (diagrams 2 and 7) and HD (diagrams 3 to 6) genes are colored red and green, respectively. See Casselton et al. (18) and Kües (90) for details. The micrograph at the bottom was obtained from Stajich et al. (86), with permission.

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Figure 5

Roles of P/R and HD genes on the formation and maintenance of the dikaryon in C. cinerea. Pheromone signaling is not required to attract mates, and hyphal fusion is mating-type independent (diagram 1). Upon fusion, nuclei enter the mycelium of the other mate and migrate until they reach a hyphal tip cell (diagram 2). During hyphal tip elongation, the two types of haploid nuclei (depicted in white and black, representing different MAT genotypes) pair at the tip cell (diagram 3), and at the place where mitosis will take place, a hook-like structure (called a clamp connection) is formed (diagram 4). The two nuclei divide synchronously: one of the nuclei divides in the direction of the clamp cell that is growing backward toward the main hyphae, while the other divides along the main hyphal axis (diagram 5). Septa are generated between the dividing nuclei. This way one nucleus stays temporarily entrapped in the clamp cell, one nucleus of the other type is enclosed in the newly formed subapical cell, and a nucleus of each type is maintained in the emerging hyphal tip cell (diagram 6). The clamp cell fuses with the subapical cell and releases the entrapped nucleus from the clamp cell, restoring the dikaryotic state of the subapical cell (diagram 7). In C. cinerea, steps controlled by P/R (diagrams 2 and 7) and HD (diagrams 3 to 6) genes are colored red and green, respectively. See Casselton et al. (18) and Kües (90) for details. The micrograph at the bottom was obtained from Stajich et al. (86), with permission.

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